Contacts of the strand formed by residues 70 - 77 (chain F) in PDB entry 2CSL
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 70 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E MSE 3.5 14.4 - - - +
60F LEU* 3.3 33.9 - - + -
66F GLY 3.8 1.8 - - - +
67F LEU 3.2 16.6 + - - +
68F SER 3.4 0.6 - - - -
69F ARG* 1.3 76.0 - - - +
71F VAL* 1.3 59.6 + - - +
72F GLN 3.6 10.8 - - - +
73F THR* 3.6 31.0 - - + -
94F PHE* 3.7 13.2 - - + -
99F PRO* 3.3 23.6 - - + +
119F CYS* 3.9 9.4 - - + -
120F VAL 3.7 2.5 - - - +
121F ALA* 3.6 11.7 - - + -
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Residues in contact with VAL 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1E MSE 4.4 3.8 - - + -
20E VAL* 3.8 26.2 - - + +
22E ALA* 3.7 24.7 - - + -
27E PHE* 3.5 36.0 - - + +
25F PHE* 4.8 1.6 - - + -
69F ARG 3.6 13.0 - - - +
70F VAL* 1.3 74.2 - - - +
72F GLN* 1.3 64.7 + - + +
99F PRO* 3.6 1.9 - - - +
100F ALA* 2.9 26.5 + - - +
120F VAL* 2.8 24.4 + - + +
121F ALA* 4.5 0.4 - - - +
122F LEU* 3.9 15.5 - - + +
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Residues in contact with GLN 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72D GLN* 5.2 1.7 + - - -
27E PHE* 3.6 37.1 - - + +
28E VAL 5.4 3.8 + - - -
72E GLN* 5.3 1.4 + - - -
118E ALA* 5.9 4.9 - - - +
119E CYS 4.7 3.8 + - - -
120E VAL* 3.9 14.8 - - - +
70F VAL* 3.6 2.0 - - - +
71F VAL* 1.3 85.2 - - + +
73F THR* 1.3 74.9 + - - +
74F THR* 4.6 9.2 + - - +
99F PRO* 4.2 0.2 - - - -
100F ALA* 3.3 13.4 - - + +
119F CYS* 3.0 8.0 - - - +
120F VAL* 2.8 53.0 + - + +
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Residues in contact with THR 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F VAL* 3.6 20.6 - - + -
72F GLN* 1.3 85.9 - - - +
74F THR* 1.3 63.1 + - - +
75F CYS* 3.8 8.9 - - - -
90F TYR* 2.7 31.1 + - + +
94F PHE* 4.1 11.4 - - + -
99F PRO* 4.3 2.2 - - + -
100F ALA 2.9 10.0 + - - +
101F ARG* 3.5 12.1 - - - +
102F ALA* 3.4 21.5 + - - +
117F VAL* 4.4 6.1 - - + -
118F ALA 3.3 7.2 - - - -
119F CYS* 3.6 8.5 - - + +
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Residues in contact with THR 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D THR* 6.2 1.1 - - + -
74E THR* 6.0 1.6 - - + -
76E PHE* 4.9 10.3 - - + -
72F GLN* 4.6 12.0 + - - -
73F THR* 1.3 75.3 - - - +
75F CYS* 1.3 62.1 + - - +
76F PHE* 3.4 37.0 - - + -
102F ALA* 3.8 15.6 - - + +
104F VAL* 6.3 0.7 - - + -
117F VAL* 3.5 3.3 - - - -
118F ALA* 2.8 38.4 + - - +
119F CYS* 5.7 0.2 - - - -
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Residues in contact with CYS 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73F THR* 3.8 12.1 - - - -
74F THR* 1.3 77.8 - - - +
76F PHE* 1.3 64.2 + - - +
77F LEU* 5.6 0.2 - - + -
86F PHE* 3.7 35.4 - - + -
90F TYR* 4.1 3.6 - - - -
101F ARG* 3.8 25.6 - - - -
102F ALA 2.8 13.8 + - - +
103F THR* 3.2 13.2 - - + +
104F VAL* 3.1 26.2 + - - +
116F GLU 3.9 3.4 - - - -
117F VAL* 4.1 13.7 - - + -
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Residues in contact with PHE 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74D THR* 4.9 15.7 - - + -
76D PHE* 4.6 10.3 - + - -
102D ALA* 4.7 14.8 - - + -
104D VAL* 3.7 28.9 - - + -
76E PHE* 4.7 5.4 - + - -
74F THR* 3.4 39.3 - - + -
75F CYS* 1.3 74.8 - - - +
77F LEU* 1.3 64.2 + - - +
104F VAL* 3.5 18.2 - - + -
106F VAL* 3.7 22.7 - - + -
109F LEU* 3.8 20.7 - - + +
115F VAL* 3.6 4.7 - - - +
116F GLU* 2.9 49.7 + - + +
117F VAL* 5.3 0.2 - - - -
118F ALA* 5.2 2.7 - - + -
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Residues in contact with LEU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45F ILE* 4.5 7.2 - - + -
75F CYS 5.2 0.2 - - - +
76F PHE* 1.3 82.3 - - - +
78F ALA* 1.3 60.6 + - - +
79F ASP 3.3 15.7 - - - +
80F MSE 4.3 6.7 - - + -
82F ASP* 4.5 0.9 - - + -
83F PHE* 3.9 46.9 - - + +
86F PHE* 3.9 22.4 - - + -
103F THR* 4.1 14.8 - - + -
104F VAL 2.9 11.0 + - - +
105F ALA* 3.2 5.6 - - + -
106F VAL* 2.8 28.4 + - - +
109F LEU* 4.3 4.0 - - - -
114F ARG 3.6 7.9 - - - +
115F VAL* 3.8 22.0 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il